Diffuse nitrate pollution in groundwater is currently considered one of the major causes of water quality degradation. Determining the sources of nitrate contamination is an important first step for a better management of water quality. Thus, the isotopic composition of nitrate (δN and δO) and boron (δB) were used to evaluate nitrate contamination sources and to identify geochemical processes occurring in the shallow and deep aquifers of the Turin-Cuneo plain (NW Italy). The study area is essentially an agricultural zone, where use of synthetic nitrogenous fertilizers and organic manure is a common practice and the connection to sewer services is locally lacking. Also livestock farming are highly developed. A groundwater sampling campaign was performed on 34 wells in the shallow aquifer and 8 wells in the deep aquifers, to analyze nitrate, chloride, boron, δN, δO and δB. Isotope data of nitrate indicate that nitrate contamination in the Turin-Cuneo plain originates from mixtures of synthetic and organic sources, slightly affected by denitrification, and manure or septic tank effluents. Moreover, boron isotopes were used to discriminate further among the main anthropogenic sources of pollution. The analyses results confirm that both animal manure and domestic sewage, especially under the city of Turin, can contribute to the nitrate contamination. The isotope analysis was also used for the evaluation of denitrification and nitrification processes: contrary to expectations, a significant denitrification phenomenon was assessed only in the shallow unconfined aquifer, especially in the Poirino Plateau, the most contaminated sector of the study area.